Degree Type


Date of Award


Degree Name

Master of Science



First Advisor

Maria G. Salas Fernandez


Carotenoids are accessory pigments that play roles in photosynthesis and photoprotection in plant leaves. Genetic studies to associate carotenoid candidate genes with variation in photosynthetic capacity however, have not been conducted. The objectives of this research project were to characterize the phenotypic variation of photosynthetic rate (A), effective quantum yield (πPSII), and photochemical quenching (qP) in sorghum (Sorghum bicolor L.), and to determine the level of association between phenotypic variation and polymorphisms in carotenoid candidate genes. A LI-COR 6400XT portable photosynthesis unit was used as a high-throughput assessment tool in all experiments. Preliminary studies were performed to evaluate experimental conditions that could potentially affect measured variation of leaf photosynthetic rate in sorghum. Results from those preliminary studies indicated that plant developmental stage, leaf section, radiation level, and CO2 concentration in the LI-COR chamber were important variables. The optimal conditions for photosynthetic measurements as determined in preliminary experiments were implemented in Linkage Disequilibrium (LD) mapping experiments. A carotenoid diversity panel consisting of 86 sorghum lines with known genetic variation for the carotenoid candidate genes Crtiso, Lcye, Hyd1, Hyd2, Zds, Ccd1, Nced3, Lcyb, Crtre, Pds, Psy1, and Psy3 was evaluated under controlled and field conditions. Genetic associations between markers in the carotenoid genes and photosynthetic phenotypes were established by GLM and MLM models which include corrections for population structure, kinship, and multiple comparisons. Multiple markers in three genes Crtiso, Ccd1, and Hyd1 were significantly associated with variation in photosynthetic rate and effective quantum yield in one or both environments. Individual markers explained between 5 to 8% of the phenotypic variation, as expected based on the genetic and physiological complexity of the trait under investigation. This study is, to our knowledge, the first investigation on the natural genetic variation in carotenoid candidate genes and their effect on the photosynthetic capacity of a crop species. This research project was also a proof of concept that LD mapping can be applied successfully to determine the genetic architecture of complex physiological traits such as photosynthesis.


Copyright Owner

Katie Jo Strand



File Format


File Size

73 pages